Contacts of the helix formed by residues 313 - 324 (chain C) in PDB entry 5AQP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 313 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C PHE* 3.6 23.2 - - - -
200C LEU* 4.2 19.1 - - + -
205C PHE* 3.3 32.4 - - + -
228C LEU* 4.0 20.9 - - + -
233C PHE* 5.8 0.9 - - + -
309C LEU 3.5 15.9 + - - +
310C PHE* 2.7 21.4 + - + +
311C ARG 3.1 0.2 - - - -
312C GLY* 1.4 75.0 - - - +
314C LEU* 1.4 64.5 + - - +
315C ASP 3.4 0.2 - - - -
316C PRO* 3.5 3.9 - - - +
317C VAL* 3.6 10.4 + - - +
346C ILE* 4.9 7.4 + - + +
349C LEU* 5.3 2.4 - - - +
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 5.2 0.2 - - + -
310C PHE 5.1 0.2 - - - +
311C ARG* 3.1 16.9 + - - +
313C THR* 1.4 83.9 - - - +
315C ASP* 1.4 60.9 + - - +
316C PRO 3.5 0.2 - - - -
317C VAL* 3.2 9.2 + - + +
318C GLU* 2.9 36.3 + - + +
349C LEU* 4.0 37.0 - - + +
350C LEU* 4.0 25.8 - - + -
353C PHE* 3.9 38.4 - - + -
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Residues in contact with ASP 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C ARG 4.5 4.5 - - - +
312C GLY* 3.4 19.0 + - - +
314C LEU* 1.4 74.8 - - - +
316C PRO* 1.3 74.9 - - + +
318C GLU* 3.2 18.6 + - - +
319C LYS* 2.9 23.0 + - - +
322C ARG* 5.6 0.3 + - - -
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Residues in contact with PRO 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C PHE* 3.5 31.4 - - + -
207C VAL* 4.2 6.5 - - + -
223C ALA* 3.4 11.3 - - + +
224C GLY* 3.7 31.6 - - - +
225C ASP* 5.5 1.6 - - + -
312C GLY 3.2 15.5 - - - +
313C THR 3.5 4.7 - - - +
315C ASP* 1.3 92.9 - - + +
317C VAL* 1.3 51.8 + - - +
319C LYS* 4.2 4.3 - - + -
320C ALA* 2.8 35.5 + - - +
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LEU* 4.2 8.9 - - + +
198C PHE* 3.8 27.1 - - + -
207C VAL* 4.0 16.8 - - + -
313C THR 3.6 14.8 - - - +
314C LEU* 3.2 14.4 + - - +
316C PRO* 1.3 76.0 - - - +
318C GLU* 1.3 57.6 + - - +
320C ALA* 3.5 1.9 + - - +
321C LEU* 3.0 30.0 + - + +
350C LEU* 4.1 8.1 - - + -
353C PHE* 3.5 34.8 - - + -
354C PHE* 4.1 16.2 - - + -
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C LEU* 2.9 22.3 + - - +
315C ASP* 3.6 17.3 - - - +
317C VAL* 1.3 75.7 - - - +
319C LYS* 1.4 57.3 + - - +
321C LEU* 3.5 9.6 + - - +
322C ARG* 3.1 42.4 + - - +
353C PHE* 3.7 30.4 - - + -
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Residues in contact with LYS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C THR 5.9 0.2 - - - +
223C ALA* 4.5 10.1 - - + -
315C ASP 2.9 16.2 + - - +
316C PRO* 3.6 8.5 - - + +
318C GLU* 1.4 77.0 - - - +
320C ALA* 1.4 56.1 + - - +
322C ARG* 3.3 29.7 + - - +
323C ASP* 2.9 43.0 + - - +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C LEU* 5.1 0.2 - - + -
207C VAL* 3.6 28.3 - - + +
209C ILE* 3.5 10.5 - - + -
221C SER* 2.7 34.0 + - - +
222C THR 5.3 0.7 - - - -
223C ALA* 4.1 11.2 - - + +
316C PRO 2.8 20.4 + - - +
317C VAL 3.7 2.5 - - - +
319C LYS* 1.4 71.4 - - - +
321C LEU* 1.4 55.6 + - - +
323C ASP* 3.3 2.7 + - - -
324C ALA* 3.0 19.8 + - - +
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C LEU* 4.8 2.2 - - + -
209C ILE* 3.5 11.6 - - + +
317C VAL* 3.0 25.7 + - + +
318C GLU* 3.7 6.3 - - - +
319C LYS 3.4 0.2 - - - -
320C ALA* 1.4 74.4 - - - +
322C ARG* 1.3 60.0 + - - +
324C ALA* 3.5 1.3 + - - -
325C LYS 3.2 3.3 + - - -
326C LEU* 2.9 43.5 + - + +
327C ASP 4.0 6.7 - - - +
328C LYS* 3.8 24.9 - - + +
331C ILE* 3.8 35.9 - - + -
353C PHE* 3.7 33.2 - - + -
354C PHE* 4.6 2.2 - - + -
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Residues in contact with ARG 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C ASP 5.6 0.4 + - - -
318C GLU* 3.1 27.8 + - - +
319C LYS* 3.4 41.2 - - - +
321C LEU* 1.3 75.9 - - - +
323C ASP* 1.4 65.3 + - - +
325C LYS* 3.1 23.7 + - - +
326C LEU 5.0 0.7 - - - -
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Residues in contact with ASP 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C LYS 4.1 5.7 - - - +
221C SER* 3.8 19.5 - - - -
222C THR 4.7 8.8 - - - +
319C LYS* 2.9 34.1 + - - +
320C ALA* 3.3 0.9 + - - -
322C ARG* 1.4 86.3 + - - +
324C ALA* 1.3 57.5 + - - +
325C LYS* 3.3 6.4 + - - +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ILE* 4.1 16.4 - - + -
220C LYS* 3.8 32.4 - - + +
221C SER* 3.5 9.9 - - - +
320C ALA 3.0 16.1 + - - +
321C LEU 4.0 4.3 - - - +
323C ASP* 1.3 75.2 - - - +
325C LYS* 1.4 70.1 + - - +
326C LEU* 3.5 16.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il